The rubber tree (Hevea brasiliensis) is a native tree from Amazon region that has great economic importance for being the largest source of natural rubber in the world. Natural rubber is used in many sectors because it is flexible, resistant, impermeable to liquids and abrasion resistant. Moreover there is no synthetic substitute with these physical properties nowadays. Rubber tree bark contains the laticifers where latex is synthesized and stored. There are two rubber biosysthesis pathways: mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP). MVA pathway has 6 enzymes and MEP has 8 enzymes involved in rubber pathway biosynthesis. Here we analyzed rubber tree bark transcriptome using Illumina platform for functional characterization and molecular marker development for breeding programs. Two different rubber tree clones were used for paired-end sequencing. We performed de novo assembly with 144 million reads using CLC Genomics Workbench generated 152 thousand contigs and N50=1.414 pb. Contigs longer than 400 pb were selected with a total of 50374 contigs without contaminants sequences. Approximately 32 thousand contigs had similarity with nr protein database and 21725 sequences were annotated in 37781 Gene Ontology terms. Also, an analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway was made with the annotated sequences. Among the 5 main categories, metabolism was the most represented. A total of 25 and 40 sequences are involved in MVA and MEP rubber biosynthesis pathways, respectively. These data are important to develop functional single nucleotide polymorphisms markers (SNPs) for rubber tree breeding programs.